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- PDB-6zgq: AceL NrdHF class 3 split intein GSH linked splice inactive varian... -

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Basic information

Entry
Database: PDB / ID: 6zgq
TitleAceL NrdHF class 3 split intein GSH linked splice inactive variant - C124A, N146A
ComponentsAceL NrdHF-1-1 Intein
KeywordsSPLICING
Function / homologyIODIDE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsHoffmann, S. / Mootz, H.D. / Kuemmel, D. / Singh, R.
Funding support1items
OrganizationGrant numberCountry
German Research Foundation (DFG)
CitationJournal: Chembiochem / Year: 2021
Title: Biochemical and Structural Characterization of an Unusual and Naturally Split Class 3 Intein.
Authors: Hoffmann, S. / Terhorst, T.M.E. / Singh, R.K. / Kummel, D. / Pietrokovski, S. / Mootz, H.D.
History
DepositionJun 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year
Revision 1.2May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: AceL NrdHF-1-1 Intein
B: AceL NrdHF-1-1 Intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,0729
Polymers37,1842
Non-polymers8887
Water3,459192
1
A: AceL NrdHF-1-1 Intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9734
Polymers18,5921
Non-polymers3813
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AceL NrdHF-1-1 Intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1005
Polymers18,5921
Non-polymers5084
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.504, 45.060, 46.281
Angle α, β, γ (deg.)65.450, 77.510, 69.350
Int Tables number1
Space group name H-MP1

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Components

#1: Protein AceL NrdHF-1-1 Intein


Mass: 18591.914 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-IOD / IODIDE ION / Iodide


Mass: 126.904 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 1.97 Å3/Da / Density % sol: 37.71 %
Crystal growTemperature: 305 K / Method: vapor diffusion, hanging drop / Details: PEG3350 25 %, Glycerol 20 %, 0.1 M MIB

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Jan 27, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 1.9→41.96 Å / Num. obs: 20988 / % possible obs: 93.6 % / Redundancy: 3.4 % / CC1/2: 0.993 / Rmerge(I) obs: 0.09 / Rpim(I) all: 0.058 / Rrim(I) all: 0.107 / Net I/σ(I): 7.1 / Num. measured all: 72086
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.9-1.943.50.411442212750.8560.2620.49289.1
9.11-41.963.10.0596011930.9940.0390.07116.395.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→41.96 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.91 / SU B: 13.883 / SU ML: 0.173 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2531 1070 5.1 %RANDOM
Rwork0.2257 ---
obs0.2272 19917 93.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 291.7 Å2 / Biso mean: 15.512 Å2 / Biso min: 4.86 Å2
Baniso -1Baniso -2Baniso -3
1--0.46 Å21.64 Å22.02 Å2
2--0.73 Å2-0.16 Å2
3---0.69 Å2
Refinement stepCycle: final / Resolution: 1.9→41.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 7 192 2639
Biso mean--51.53 46.15 -
Num. residues----307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0192575
X-RAY DIFFRACTIONr_bond_other_d0.0010.022414
X-RAY DIFFRACTIONr_angle_refined_deg1.411.9513490
X-RAY DIFFRACTIONr_angle_other_deg0.72635616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4445327
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.44125.691123
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.84415478
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.135158
X-RAY DIFFRACTIONr_chiral_restr0.0910.2389
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022951
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02555
X-RAY DIFFRACTIONr_rigid_bond_restr2.2134989
X-RAY DIFFRACTIONr_sphericity_free531
X-RAY DIFFRACTIONr_sphericity_bonded24.09655101
LS refinement shellResolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.379 88 -
Rwork0.288 1400 -
all-1488 -
obs--89.32 %

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